Abstract
The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.
Highlights
Genome assembly has been an area of interest for research groups worldwide since the initiation of the Human Genome Project in 1990
The complete mitochondrial genomes of about one-third Asian macaques [1,2,3] have been sequenced and assembled up-to-date. These include the mitogenomes of the Indian rhesus macaque (Macaca mulatta) [4,5,6], Chinese rhesus macaque (M. mulatta lasiota) [7], longtail/crab-eating macaque (M. fascicularis) from Mauritius, Malaysia and Indochina [6, 8], Tibetan macaque (M. thibetana) [6, 9], Assam macaque (M. assamensis) [10], lion-tailed macaque (M. silenus) [6], stump-tailed macaque (M. arctoides) [6, 11], Tonkean macaque (M. tonkeana) [6] and Japanese macaque (M. fuscata) [12], leaving only the mitogenome of Taiwanese (Formosan) macaque (M. cyclopis) remain unsequenced
Our results show that its organization and gene order are very similar to those of other macaques and phylogeny based on mitogenomes of several macaque species supports a close relationship of M. cyclopis to M. mulatta mulatta and M. mulatta lasiota in the fascicularis group
Summary
Genome assembly has been an area of interest for research groups worldwide since the initiation of the Human Genome Project in 1990. The complete mitochondrial genomes (mitogenomes) of about one-third Asian macaques [1,2,3] have been sequenced and assembled up-to-date. These include the mitogenomes of the Indian rhesus macaque (Macaca mulatta) [4,5,6], Chinese rhesus macaque (M. mulatta lasiota) [7], longtail/crab-eating macaque (M. fascicularis) from Mauritius, Malaysia and Indochina [6, 8], Tibetan macaque (M. thibetana) [6, 9], Assam macaque (M. assamensis) [10], lion-tailed macaque (M. silenus) [6], stump-tailed macaque (M. arctoides) [6, 11], Tonkean macaque (M. tonkeana) [6] and Japanese macaque (M. fuscata) [12], leaving only the mitogenome of Taiwanese (Formosan) macaque (M. cyclopis) remain unsequenced. The mitogenome of Taiwanese macaque could be an important piece in solving the puzzle of evolution of the fascicularis group
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